KorfLab/lyman2020

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Created over 4 years ago
Updated over 2 years ago

KorfLab/lyman2020

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Custom scripts for Lyman et al (2020)

StochHMM

A Hidden Markov Model Application and C++ Library for Rapid and Flexible Development of HMMs

SNAP

Gene prediction software

CEGMA_v2

The final version 2 release of our software to detect core genes in eukaryotic genomes

Assemblathon

Code that was used in the Assemblathon 1 and 2 projects

LearnGit

Let's Learn Git

Perl_utils

Miscellaneous Perl scripts and modules used by people in the Korf lab

imeter

2022 reboot of IME project

Centromere_repeat_paper

Code used to generate data for our analysis of centromeric repeats

FRAG_project

To contain code and data files for the Fragmentation project, investigating shattered chromosome phenotypes in Arabidopsis thaliana

setup

How to set up your work environment

CEGMA_v3

CEGMA (Core Eukaryotic Genes Mapping Approach), for building a highly reliable set of gene annotations in the absence of experimental data.

Rosalind

Solutions to Rosalind problems

grimoire

Biological sequence analysis tools

datacore

Standardized protocols and datasets for some model organisms

genomikon

Genomic sequence analysis library & apps

spitfire

learning-snakemake

Suecica

Scritps written for research on A. suecica for Luca Comai's lab

algorithms

Sickle

genDL

Genomic experiments in Deep Learning

Jupyter Notebook

Genesmith

Gene finder mixing genomic and protein information

learning-go

learning-C

DupHMM

An easy to use hidden Markov model-based copy number variant identifier

Milk-DNase-Seq-Project

Analysis of milk DNase-Seq data in mouse and human

diseasy

ago

julie

Bioinformatics experiments with Julia

unix_and_perl

learning-conda

IME

A new code base for the IME project.

korflab.github.io

Ploidamatic

StochHMM-based decoder for detecting copy number from alignments

grimoire2